The Shadow War
by AlphaGuardian
Summary: OC's welcome and accepted. The CIA's special ops unit, Cemetery Wind, has discovered a relic of an ancient empire at the edge of the solar system. When they use it, they find a new universe, and Transformers. Allying themselves with a group called Cerberus, they fight to rid the galaxy of Transformers. But some things are too good to be true...


Prologue: Distant Thunder

_They say we're not alone in this universe._

_I believe them. I've seen first contact, and it wasn't pretty._

_That's why the CIA's special ops unit, Cemetery Wind, exists. To hunt down aliens._

_And kill them._

_They call me Ghost. I'm one of the best in Cemetery Wind._

_But now, Cemetery Wind has a new purpose. Saving human lives in another galaxy from the Transformers. Many stories interconnect and collide here, and all will be told._

_Without all the black ink._

_Omega. Omega Nebula._

"Kid, I don't know who the fuck you think you're dealing with," Ghost said coldly, "but I've killed things twenty times your size, and with ten times the balls you got. So I suggest you get the fuck out of my way, because I'll shoot you dead right now and not feel one bit bad."

The kid, who couldn't have been more than eighteen or nineteen years old, didn't back down. Deviant, Ghost's closest friend, was at his side, ready to put the kid down if need be.

"I can take you, no sweat." The kid started. "You don't scare me. Come on. Come at-"

A gunshot rang out, a brass casing fell to the ground, and then the kid followed. He now sported a hole in the side of his head. Ghost scowled as he replaced his pistol in its holster.

"Deviant, find the commander. I want reports every ten minutes. You see him, radio your location, and follow him. When I give the signal, move in, and secure. Do not harm him unless absolutely necessary. He's in with Prime. We can't deal with him yet. Move out."

"Sir." Deviant said as he walked away.

Ghost initiated a link to his associate.

"Your intel had better be good." The former started.

"_It is. I assure you, Cerberus looks after its own. He's there. Now, find him, and I'll make it worth your while._"

"I'm not in it for the money. I want the Transformers dead."

"_And they will be. In due time, Ghost._"

"I'm a patient man, Harper, but don't push it."

"_I expect good results from this. Cerberus does not tolerate failure well._"

"Neither does Cemetery Wind. We'll get the Commander."

"_Good._"

Ghost cut the link, and meandered through the streets, hunting for his target. Commander Shepard had been running around the galaxy ever since the CIA's special ops unit, Cemetery Wind, found a dormant Mass Relay, and activated it, which had sent them to what the locals called the Terminus Systems. They had been found by Cerberus, and when a mutual hatred of Transformers was established, Cemetery had agreed to work with Cerberus, but remain independent of the latter.

As he casually walked the streets, he nearly ran over a young woman. As he skirted to the side to avoid colliding with her, he caught a look at her face, and recognized her instantly. She was Shadow, a former Cemetery operative. They had once been friends, when Shadow was in Cemetery Unit, and Ghost had thought very highly of her, almost to the point of that dreaded feeling: love. But he had whisked those thoughts away when she deserted. He now thought about putting a bullet through her head, but decided against it, seeing as it might draw the Commander's attention and allow him to escape, so he just walked on.

From the look on her face, Shadow had recognized him, too.

"_Deviant here. No sign of the Commander. Will keep looking._" He reported right on the mark.

"Good copy. Just saw a former Cemetery operative. No need to worry, there was no conflict."

"_If it's Shadow you're talking about, then I saw her, too._"

"Let's just find the Commander and get out of here. I have a bad feeling about this place."

"_Me too. Deviant out._"

The duo continued their searches, and soon found the Commander in a club called Afterlife. He was talking to an Asari, who Ghost had learned ran Omega.

"Deviant, I've found him. Sending coordinates."

"_Roger. On my way._"

Ghost sent his location, and watched the commander from the shadows. He conversed with the Asari, Aria, for a few more minutes before leaving for the docks. Thankfully, he was alone.

"He's on the move."

"I know." Deviant said as he walked up behind Ghost.

"Good. Let's move. We'll take him down in the docking area. Quick and clean."

"Yes, sir."

As Shepard walked into the docking bay, headed for the SSV Normandy SR-1, the two Cemetery operatives closed the gap. Just as they were about to take him down, someone blew their cover.

"BEHIND YOU!" A female voice shouted.

"Damnit!" Ghost shouted as the shocked Commander turned.

Shadow had followed _them_. The hunters had become the hunted.

_I should have killed her when I had the chance._ Ghost thought as he brought out his pistol and shot at the ex-Cemetery operative.

In his frustration, he missed all three shots. Deviant was taking the Commander on in hand-to-hand combat, and it looked like they were dead even. So Ghost decided to deal with Shadow.

He grinned as he put his pistol away, ready for a straight fistfight.

"I can take you myself." He told her.

She remained silent, as was typical.

_She's stronger than she looks. I have to be careful here._ He thought.

"Alright then. Ladies first." He said.

They circled each other once before Shadow lashed out with a vicious right hook, which Ghost countered easily. He countered with a feint jab to her midsection, which he complimented with a left hook in the side of her head, which she saw through.

He had to end this quick. Deviant could not be allowed to take down Shepard alone. It would be an insult to Ghost if he didn't keep his word to the Illusive Man. He had said that they would both bring the Commander down. If he didn't help Deviant, Ghost would destroy his own honor.

He lashed out with a kick, which Shadow dodged, but then he pushed off of the ground with his hands, and slammed both of his boots into her gut roundhouse-style. A clean hit. He had her pinned down, and knocked her out with a few more punches.

Deviant had yet to deal with Shepard, so Ghost leaped to his side, and the fight paused for a moment as Shepard sized up his odds.

"Oops. Your help is gone. Too bad for you." Ghost said smugly.

He stayed silent. Then Ghost saw him reaching for his belt, and a grenade. He leaped forward, smashed his knee into the Commander's gut, and brought both fists down on his head, which then smacked against the ground, jarring him, and allowing Ghost and Deviant to bind his hands so he couldn't escape.

"Nice work. Let's get to the ship. No need to keep the boss waiting now." Ghost said.

They hauled him away as Shadow came to. When she saw this scene, she relayed a burst message to Optimus Prime, informing him of Shepard's capture. The Autobot leader told her not to pursue them, and that they needed a plan before they attempted any kind of rescue. She left for her shuttle, and went to find the Autobots.

_Cerberus shuttle._

Ghost and Deviant hauled Shepard into the shuttle, and Deviant sat in the pilot's seat and started it up.

"File the report. I'll take the Commander back to the cargo bay." Ghost said.

"Sir."

As Deviant set up the comm channel, Ghost took Shepard to the small cargo bay, and left him in the middle of the room as he leaned in the corner.

"Why me?" He demanded. "Who are you working for?"

"No one."

"You're lying."

"I'm not getting paid for this."

"Then who sent you after me?"

"Someone with a lot of influence."

"Why?"

"You already know."

"No, I don't."

"Do. Not. Fuck. With me. I know that you know where he is."

"Who?"

"Prime."

"I don't know-"

Ghost walked over and slammed his boot into the Commander's gut. As he doubled over in pain, Ghost grabbed a knife and rested it on the back of his neck.

"Where. Is. Optimus Prime?"

He coughed and sucked in a gasp of air.

"You won't kill me." He said. "Whoever you're working with won't let you, will they?"

"No, they won't. But that doesn't mean I won't make you suffer. Now where is Prime?"

"_Ghost._" The Illusive Man said from behind him.

He turned and acknowledged the latter's presence, as Deviant had come back with the holo-comm still active.

"Illusive Man." Shepard spat.

"_Ghost, Deviant, leave._"

"Fine. But if he escapes, it's on you." Ghost said as the two Cemetery operatives left.

They sat in the cockpit as the shuttle sped towards the Cerberus base where Shepard would be dropped off, and the Cemetery duo would get their new mission.

"What do you think comes next?" Deviant asked.

"Either of two things: Cerberus betrays us, or we go hunting again, probably for someone else who might know about the bots."

"Yeah."

"Hope for the best, but expect the worst."

"I'm always ready, Ghost."

"Good. I'd hate to lose you after all we've been through together."

"It's been rough."

"But we made it through, and killed a few Transformers as well."

"Remember back in Shanghai, when we dropped that one that transformed into an Abrams?"

"Don't get me started on that. I hated that thing."

"Better go check in on the boss and the Commander, huh?"

"Yeah. I got it."

Ghost got up and walked back, finding Shepard seemingly asleep. He knew better, though. He was probably faking it. He stomped his boot on the floor, and the Commander jolted up.

_So he really was sleeping. Stupid move, Commander._ He thought.

He simply smirked and walked away. They would arrive at the Cerberus base soon enough, and she wouldn't be their problem anymore. He sat back down in the cockpit, and when he closed his eyes to let the day roll off of him, he saw Lockdown, Cemetery's former 'key asset'. He was remembering a conversation he had had with the robot bounty hunter.

"_The problem with loyalty to the cause is that the cause always betrays you. Do you understand that, human?_"

"_Perfectly. When we aren't needed anymore, our higher-ups dispose of us. Simple as that._" Ghost had responded.

"_Then you are more prepared than most. Better to see it coming than be caught off-guard. Remember that._"

Ghost had been able to hold a conversation, purely business of course, with the bounty hunter when they worked together, and as it seemed, Lockdown respected Ghost for his willingness to get the job done no matter the cost.

_The cause always betrays you._

_When will Cerberus betray me? And will I see it coming? What will I do then?_ He wondered as the shuttle approached the Cerberus base.

**Okay, now that that's taken care of, announcements!**

**I am accepting OC's, as stated in the description. I have made a few restrictions and notes at the end of the chapter, so take not of them as well.**

**If anyone would like to submit an OC, here's the info I need:**

**Name:**

**Age:**

**Race (If from Mass Effect Universe):**

**Gender:**

**Physical build:**

**Sexuality (Homo-, hetero-, or bisexual):**

**Appearance:**

**Notable Traits (Scars, deformities, and the like.):**

**Universe of Origin (Transformers or Mass Effect):**

**Home Country/Planet (For Transformers and Mass Effect Universes, respectively):**

**Affiliation:**

**Callsign (Required for Cemetery Wind members, optional for others):**

**Take on Conflict (Pro- or Anti-Transformers, or somewhere in the middle):**

**Personality:**

**Background:**

**Important Notes to Consider:**

**For Affiliation, you can have a character from, say, the US military, for Transformers, or the Alliance military, for Mass Effect. You can even have deserters from different factions, or non-military characters. Make your submissions as unique as possible!**

**For Take on Conflict, You don't have to stick with what is established. You could have a Cerberus character that is firmly for working with the Transformers, but maybe only in a way that benefits humans, in keeping with Cerberus' "humanity first, rest of the galaxy can kiss my ass" mentality. Or you could have an Alliance soldier who would like nothing more than to see all Transformers gone. As before, be as unique as you can!**

**For Race, please try to keep non-human entries to a minimum. I'm going to find it hard to work them into the story. I will try my best, but please cut me some slack. I'd say no more than one or two non-human entries.**

**(IMPORTANT) I will not accept entries for Cybertronians (Transformers). I really don't want to have a thousand Transformers on my hands. The odds need to be against them. So no Transformers, period. Sorry.**

**For those from Cemetery Wind, they are going to be separate from Ghost and Deviant. They are allowed to be acquainted with the duo, but they will not travel with Ghost and Deviant. OC Cemetery operatives will get separate chapters, and **_**may**_** encounter Ghost and Deviant once in a great while.**

**Also for Cemetery Wind characters: They are working with Cerberus. Keep that in mind before jumping on the bandwagon.**

**One final note for Cemetery Wind members. I will have a link to a Google Doc for their weapons on my profile. Please PM me your choices, since some are restricted. (Once the Doc is finished, I will make a link.**

**I will try to group characters as best I can, but if you don't like the teams, say something. Make suggestions. PLEASE!**

**Relationships between characters may appear, but only with the express consent of both character's creators. So I will ask before anything happens. (The exception is for characters owned by EA and Bioware, like Shepard. That falls to me [the writer] and the creator of the OC.)**

**You control your characters (for the most part), if you don't like something, like the way I portray your character, tell me! I'll do what I can, but some things cannot be avoided. (Yes, some OC's may die, but I will try to not have that happen.)**

**I will also be creating a companion story with Cerberus Person of Interest files for every character submitted. So check that out, too! It may reveal characters that have yet to appear in the book.**

**Thanks in advance for any characters submitted!**

**-AG. **


End file.
